User: raf4

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raf420
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r***@cumc.columbia.edu

Posts by raf4

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
... Dear Ryan, Thank you for your reply, Best wishes, Rich ...
written 4 months ago by raf420
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Comment: C: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
... Dear Gordon,' Thank you as always for your helpful reply. I will ask our sequencing core to align with Rsubread, and if not do it myself. Best wishes, Rich ...
written 4 months ago by raf420
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Comment: C: Use of pseudoalignment estimated counmts as input to edgeR and Limma-Voom
... Steve, Thanks. I know that procedure. Gordon has written :""In my opinion, there is no good way to do a DE analysis of RNA-seq data starting from the TPM values. TPMs just throw away too much information about the original count sizes." I am asking if pseudoalignment algorithms also lose that inf ...
written 4 months ago by raf420
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Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
... Dear List, Our sequencing core recently switched from STAR to Kallisto. The genewise output was given as both TPM values and counts. Gordon Smyth has written that TPMs should not be used as input to EdgeR. In a recent paper (F1000 Research 2016,4:1521) Soneson, Love, and Robinson have presented ev ...
edger tpm rnaseq-quantification written 4 months ago by raf420 • updated 4 months ago by Gordon Smyth37k
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Comment: C: Differential expression analysis starting from TPM data
... Jim, From the original Kallisto paper,Bray, et al., Nature Biotech 34, p.525, online methods: "The transcript abundances are output by Kalllisto in transcripts per million (TPM) units". I will rephrase my question as a separate query, incorporating your point about estimated counts. Thank you as al ...
written 4 months ago by raf420
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Comment: C: Differential expression analysis starting from TPM data
... Jim, Thank you for the correction with respect to how to ask my question. One of the files I received from the sequencing core was labeled tpm_values_genes_kallisto.txt, which gave me the impression that tpm was teh primary quantity. Best wishes, Rich ...
written 4 months ago by raf420
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Comment: C: Differential expression analysis starting from TPM data
... Jim, Thank you for the correction with respect to how to ask my question. One of the files I received from the sequencing core was labeled tpm_values_genes_kallisto.txt, which gave me the impression that tpm was teh primary quantity. Best wishes, Rich ...
written 4 months ago by raf420
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Comment: C: Differential expression analysis starting from TPM data
... Dear Gordon and Everybody, Our sequencing core recently switched from STAR to Kallisto so that I either have to work from their TPM values or align the fastq files to the genome myself (I would use Rsubread). Is it recommended to recover the counts from the Kallisto TPMs with tximport? As I underst ...
written 4 months ago by raf420
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Comment: A: Error message with Voom with blocked design matrix
... Dear Gordon. I am sorry I confused "warning" for "error". Thank for answering my question. duplicateCorrelation worked just fine. Best wishes, Rich ...
written 13 months ago by raf420 • updated 13 months ago by Gordon Smyth37k
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Comment: C: Error message with Voom with blocked design matrix
... Dear Aaron, Thank you. I kept my note short to fit in the character limit. Gordon answered my question below. Best wishes, Rich ...
written 13 months ago by raf420 • updated 13 months ago by Gordon Smyth37k

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Popular Question 13 months ago, created a question with more than 1,000 views. For Problem running featurecounts in Rsubread on GFF file

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